1. Field of the Invention
The present invention relates to a method and system for predicting pathways (biological pathways) of genes that serve the same biological purpose, and more particularly, to a method and system for predicting pathways of genes that serve the same biological purpose using gene expression pattern data and protein-protein interaction (PPI) data.
2. Discussion of Related Art
When mechanism of development or pathway of a disease such as cancer is known, it is possible to cure the disease by treating genes on the pathway. However, it requires considerable time and cost to identify the pathways one by one through biological experiments.
It would be very helpful in finding cures for diseases if significant pathways could be predicted from data derived from experiments that can be performed on a large scale and do not require numerous trials.
Meanwhile, since a sequence of genes was identified by the human genome project, the study and analysis of the functions of genes, known as functional genomics, has attracted considerable attention. Functional genomics has developed remarkably thanks to DNA chips and protein interactions which facilitate large-scale experimentation. Such large-scale experimentation has helped to study and analyze groups or pathways of genes that have the same biological function and purpose rather than predict functions of individual genes.
Typically, a method of clustering a gene using an expression pattern of mRNA has been used, but it merely provides information translated by genes which express an identical function bound into one, and thus it is difficult to get information about relation between genes.
Accordingly, research into a way to derive more accurate information about genes is as active as ever.
For example, “Discovering Molecular Pathways from Protein Interaction and Gene Expression Data” by E. Segal, H. Wang & D. Koller, ISMB 2003, Jun. 29-Jul. 3, 2003, Bioinformatics Vol. 19(sup), pages i264-i272, July 2003, discloses a method for searching groups of genes on the same biological pathway from a large amount of gene expression data and PPI data. While this method yields more accurate results than the existing clustering method based on the MRNA expression pattern, like the gene clustering method, it is focused on discovering genes which have a possibility of being on the same pathway rather than obtaining information about relationships between individual genes.
“Functional topology in a network of protein interactions” by Natasa Przulj, Dennis A. Wigle & Igor Jurisica, Bioinformatics, volume 20, number 3, pages 340-348, 2004 (this article is hereby incorporated in the present invention by reference), discloses a method of searching for a biological pathway using PPI data. According to this article, the PPI data are expressed using an interaction graph, and a biological pathway is searched for using a similar shortest path algorithm in the graph. However, since there is not much actual PPI data, there is a limit to the number of pathways that can be obtained, and thus the results of this experimental method have low reliability.
While researching a solution to the foregoing problems that would enable more accurate prediction of a biological pathway of genes, the present inventors discovered that prediction of a biological pathway by using mRNA expression pattern data and PPI data obtained by the DNA chip method yields more accurate and reliable experimental results because two biological experimental results are combined to obtain high reliability and more information enables to generate more accurate results. This discovery led to the present invention.